The Cs value that you are referring to, is used when computing base shear as per the Equivalent Lateral Force method and is not used in a response spectrum analysis. For response spectrum analysis, you may refer to the section 12.9 of ASCE7-05. The factor that you use for X ( or Y or Z ) while defining a spectrum loading is referred to as a direction factor and is used to factor the input spectrum data.
You will also find lot of good information on response spectrum analysis at
communities.bentley.com/.../2044.staad-pro-response-spectrum-faq.aspx